NAKAI Lab.

Laboratory of Functional Analysis in silico

Human Genome Center
The Institute of Medical Science
The University of Tokyo

Latest publications

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Alexis Vandenbon, Yutaro Kumagai, Mengjie Lin, Yutaka Suzuki, and Kenta Nakai. Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation. Genome Biol., accepted.

Naoya Fujita, Shinji Mizuarai, Katsuhiko Murakami, and Kenta Nakai. Biomarker discovery by integrated joint non-negative matrix factorization and pathway signature analyses. Sci. Rep. 8, 9743 (2018).
(full text)

Phit Ling Tan, Yosvany López, Kenta Nakai, and Ashwini Patil, TimeXNet Web: Identifying cellular response networks from diverse omics time-course data. Bioinformatics, in press.
(PubMed)

Yasuo Ouchi, Ashwini Patil, Yusuke Tamura, Hiroshi Nishimasu, Aina Negishi, Sudip Kumar Paul, Naoki Takemura, Takeshi Satoh, Yasumasa Kimura, Makoto Kurachi, Osamu Nureki, Kenta Nakai, Hiroshi Kiyono, Satoshi Uematsu. Generation of tumor antigen-specific murine CD8+ T cells with enhanced anti-tumor activity via highly efficient CRISPR/Cas9 genome editing. Int. Immunol., 30(4) 141-154 (2018).
(full text) Editor's choice

Myungjin Moon and Kenta Nakai, Integrative analysis of gene expression and DNA methylation using unsupervised feature extraction for detecting candidate cancer biomarkers. J. Bioinf. Comput. Biol., 16(2), 1850006 (2018).
(abstract)

Masashi Fujita, Nagahide Matsubara, Ikuo Matsuda, Kazuhiro Maejima, Ayako Ohsawa, Tomoki Yamano,, Akihiro Fujimoto, Mayuko Furuta, Kaoru Nakano, Aya Oku-Sasaki, Hiroko Tanaka, Yuichi Shiraishi, Raúl Mateos, Kenta Nakai, Satoru Miyano, Naohiro Tomita, Seiichi Hirota, Hiroki Ikeuchi, Hidewaki Nakagawa, Genomic landscape of colitis-associated cancer indicates the impact of chronic inflammation and its stratification by mutations in the Wnt signaling. Oncotarget 9, 969-981 (2018).
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Matija Brozovic, Christelle Dantec, Justine Dardaillon, Delphine Dauga, Emmanuel Faure, Mathieu Gineste, Alexandra Louis, Kazuhiro Nitta, Magali Naville, Jacques Piette, Céline Scornavacca, Paul Simion, Renaud Vincentelli, Maelle Bellec, Sameh Ben Aicha, Marie Fagotto, Marion Guéroult-Bellone, Maximilian Haeussler, Edwin Jacox, Elijah Lowe, Mickael Mendez, Wendy Reeves, Alexis Roberge, Alberto Stolfi, Rui Yokomori, C. Titus Brown, Christian Cambillau, Lionel Christiaen, Frédéric Delsuc, Emmanuel Douzery, Rémi Dumollard, Takehiro Kusakabe, Kenta Nakai, Hiroki Nishida, Yutaka Satou, Billie Swalla, Michael Veeman, Jean-Nicolas Volff, and Patrick Lemaire, ANISEED 2017 : Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucl. Acids Res., 46(D1), D718-D725 (2018); published on 15 Nov. 2017.
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Ayako Suzuki, Shin Kawano, Toutai Mitsuyama, Mikita Suyama, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, and Yutaka Suzuki, DBTSS/DBKERO for integrated analysis of transcriptional regulation. Nucl. Acids Res., 46(D1), D229-D238 (2018); published online on Nov. 8, 2017.
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Motohiko Kadoki, Ashwini Patil, Cornelius C. Thaiss, Donald J. Brooks, Surya Pandey, Deeksha Deep, David Alvarez, Ulrich H. von Andrian, Amy J. Wagers, Kenta Nakai, Tarjei S. Mikkelsen, Magali Soumillon, and Nicolas Chevrier, Organism-level analysis of vaccination reveals networks of protection across tissues. Cell 171(2), 398-413.e21 (2017),, published September 21, 2017.
(abstract)

Jong-Hun Lee, Sung-Joon Park, Kenta Nakai, Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s, Sci. Rep. 7, 11295 (2017).
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Yosvany López, Alexis Vandenbon, Akinao Nose, and Kenta Nakai, Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster, PeerJ, 5, e3389 (2017).
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Yasunori Sasakura, Yosuke Ogura, Nicholas Treen, Rui Yokomori, Sung-Joon Park, Kenta Nakai, Hidetoshi Saiga, Tetsushi Sakuma, Takashi Yamamoto, Shigeki Fujiwara, and Keita Yoshida, Transcriptional regulation of a horizontally transferred gene from bacterium to chordate. Proc. Royal Soc. B. 283(1845), pii: 20161712 (2016).
(PubMed)

Josep Basha Gutierrez and Kenta Nakai, A study on the application of topic models to motif finding algorithms. BMC Bioinformatics 17(Suppl. 19), 1364 (2016).
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Myungjin Moon and Kenta Nakai, Stable feature selection based on the ensemble L₁-norm support vector machine for biomarker discovery. BMC Genomics 17(Suppl. 13), 3320 (2016).
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Satoru Onizuka, Takanori Iwata, Sung-Joon Park, Kenta Nakai, Masayuki Yamato, Teruo Okano, and Yuichi Izumi, ZBTB16, a downstream target gene of Osterix, regulates osteoblastogenesis of human multipotent mesenchymal stromal cells. J. Cell. Biochem., 117(10), 2423-2434 (2016).
(PubMed)

Kazuhiro Fukumura, Shunichi Wakabayashi, Naoyuki Kataoka, Hiroshi Sakamoto, Yutaka Suzuki, Kenta Nakai, Akila Mayeda, and Kunio Inoue, The exon junction complex controls the efficient and faithful splicing of a subset of transcripts involved in miotic cell-cycle progression. Int. J. Mol. Sci., 17(8), 1153 (2016).
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Sung-Joon Park and Kenta Nakai, Chapter 7: Computational inference of gene regulation from whole-transcriptome analysis of early embryos. in (Ivan V. Ivanov, Xiaoning Qian, and Ranadip Pal eds.) Emerging Research in the Analysis and Modeling of Gene Regulatory Networks, pp.241-279, IGI Global, ISBN: 9781522503538 (2016).

Yuzuru Sasamoto, Ryuhei Hayashi, Sung-Joon Park, Mihoko Saito-Adachi, Yutaka Suzuki, Satoshi Kawasaki, Andrew Quantock, Kenta Nakai, Motokazu Tsujikawa, and Kohji Nishida, PAX6 isoforms, along with reprogramming factors, differentially regulate the induction of cornea-specific genes. Sci. Rep., 6, 20807 (2016).
(abstract)

Sung-Joon Park, Mihoko Saito-Adachi, Yusuke Komiyama, and Kenta Nakai, Advances, practice, and clinical perspectives in high-throughput sequencing, Oral Diseases, 22(5), 353-364 (2016).
(PubMed)

Rui Yokomori, Kotaro Shimai, Koki Nishitsuji, Yutaka Suzuki, Takehiro G. Kusakabe, and Kenta Nakai, Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis. Genome Res., 26, 140-150 (2016).
(abstract)

Sung-Joon Park, Yusuke Komiyama, Hirofumi Suemori, Akihiro Umezawa, and Kenta Nakai, OpenTein: a database of digital whole-slide images of stem cell-derived teratomas. Nucl. Acids Res., 44(D1), D1000-D1004 (2016).
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Yosvany López, Kenta Nakai, and Ashwini Patil, HitPredict version 4 - comprehensive reliablity scoring of physical protein-protein interactions from more than 100 species, DATABASE, 2015, bav117 (2015).
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Kuo-ching Liang, Ashwini Patil, and Kenta Nakai, Discovery of intermediary genes between pathways using sparse regression. PLoS One, 10(9), e0137222 (2015).
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Jong-Hun Lee, Sung-Joon Park, and Kenta Nakai, An integrative approach for efficient analysis of whole genome bisulfite sequencing data. BMC Genomics 16(Suppl 12), S14 (2015)
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Josep Basha Gutierrez, Martin Frith, and Kenta Nakai, A genetic algorithm for motif finding based on statistical significance. Bioinformatics and Biomedical Engineering (Third International Conference, IWBBIO 2015, Granada, Spain, April 15-17, 2015, Proceedings, Part I), Springer, LNCS 9043, pp.438-449 (2015).

Ayako Suzuki, Hiroyuki Wakaguri, Riu Yamashita, Shin Kawano, Katsuya Tsuchihara, Sumio Sugano, Yutaka Suzuki, and Kenta Nakai, DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data. Nucl. Acids Res., 43, D87-D91 (2015).
(full text).

Sung-Joon Park, Katsuhiko Shirahige, Miho Ohsugi and Kenta Nakai, DBTMEE: a database of transcriptome in mouse early embryos. Nucl. Acids Res., 43, D771-D776 (2015).
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Lucky R. Runtuwene, Kaori Noguchi, Akinori Tokunaga, Takashi Kobayashi, Kenta Nakai, and Yuki Eshita, Vector competence of Aedes aegypti to dengue virus. Urban Pest Management, 4(1), 1-14 (2014),

Ashwini Patil and Kenta Nakai, TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles, BMC Syst. Biol., 8(Suppl.4), S2 (2014).
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Yosvany López, Alexis Vandenbon, and Kenta Nakai, A Set of Structural Features Defines the Cis-Regulatory Modules of Antenna-Expressed Genes in Drosophila melanogaster, PLoS One 9(8), e104342 (2014).
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Sanaz Firouzi, Yosvany López, Yutaka Suzuki, Kenta Nakai, Sumio Sugano, Tadanori Yamochi and Toshiki Watanabe, Development and validation of a new high-throughput method to investigate the clonality of HTLV-1-infected cells based on provirus integration sites, Genone Medicine, 6, 46 (2014).
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Kenta Nakai, Overview of Bioinformatics Research in Japan, Asia Pacific Biotech, 18(9), 35-37 (2014).

Kyungtaek Lim, Ichizo Kobayashi, and Kenta Nakai, Alterations in rRNA-mRNA interaction during plastid evolution, Mol. Biol, Evol., 31(7), 1728-1740 (2014).
(PubMed)

Sung-Joon Park, Terumasa Umemoto, Mihoko Saito-Adachi, Yoshiko Shiratsuchi, Masayuki Yamato, and Kenta Nakai, Computational promoter modeling identifies the modes of transcriptional regulation in hematopoietic stem cells, PLoS One, 9(4), e93853 (2014).
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Alok Sharma, Abdollah Dehzangi, James Lyons, Seiya Imoto, Satoru Miyano, Kenta Nakai, and Ashwini Patil, Evaluation of sequence features from intrinsically disordered regions for the estimation of protein function, PLoS One, 9(2), e89890 (2014).
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Asmaa Elzawahry, Ashwini Patil, Yutaro Kumagai, Yutaka Suzuki, and Kenta Nakai, Innate immunity interactome dynamics, Gene Regulation and Systems Biology, 8, 1-15 (2014)
(abstract & pdf)

Kuo-ching Liang, Yutaka Suzuki, Yutaro Kumagai, and Kenta Nakai, Analysis of changes in transcription start site distribution by a classification approach, Gene, 537(1), 29-40 (2014); published online 31 December 2013
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Sung-Joon Park, Makiko Komata, Fukashi Inoue, Kaori Yamada, Kenta Nakai, Miho Ohsugi and Katsuhiko Shirahige, Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis, Genes Dev., 27(24), 2736-2748 (2013).
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Ashwini Patil, Yutaro Kumagai, Kuo-ching Liang, Yutaka Suzuki, and Kenta Nakai, Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response, PLoS Comput. Biol., 9(11), e1003323 (2013); Epub Nov.7, 2013
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Yosvany López, Ashwini Patil, and Kenta Nakai, Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana, BMC Systems Biol., 7(Suppl 3): S10 (2013).
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Yasunori Sasakura, Nicolas Sierro, Kenta Nakai, Kazuo Inaba, and Takehiro G. Kusakabe, Chapter 4: Genome structures, functional genomics, and proteomics in ascidians, in (Denny, P. & Kole, C. eds.) Genome mapping and genomics in laboratory animals, pp.87-132, Springer (2013).

Yuko Makita and Kenta Nakai, Chapter 8: Bacillus subtilis transcriptional network, in (M. Madan Babu ed.) Bacterial Gene Regulation and Transcriptional Networks, pp.155-165, Caister Academic Press (ISBN: 978-1-908230-14-0) (2013)

Rie Kusakabe, Saori Tani, Koki Nishitsuji, Miyuki Shindo, Kohji Okamura, Yuki Miyamoto, Kenta Nakai, Yutaka Suzuki, Takehiro G. Kusakabe, and Kunio Inoue, Characterization of the compact bicistronic microRNA precursor, miR-1/miR-133, expressed specifically in Ciona muscle tissues, Gene Expression Patterns, 13(1-2), 43-50.(2013)
(PubMed)

Manabu Ozawa, Miki Sakatani, JiQiang Yao, Savita Shanker, Fahong Yu, Riu Yamashita, Shuichi Wakabayashi, Kenta Nakai, Kyle B Dobbs, Mateus J. Sudano, William G. Farmerie, and Peter J. Hensen, Global gene expression of the inner cell mass and trophectoderm of the bovine blastcyst, BMC Dev. Biol., 12, 33 (2012)
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Naganari Ohkura, Masahide Hamaguchi, Hiromasa Morikawa, Kyoko Sugimura, Atsushi Tanaka, Yoshinaga Ito, Motonao Osaki, Yoshiaki Tanaka, Riu Yamashita, Naoko Nakano, Jochen Huehn, Hans-Joerg Fehling, Tim Sparwasser, Kenta Nakai, and Shimon Sakaguchi, T cell receptor stimulation-induced epigenetic changes and Foxp3 expression are independent and complementary events required for Treg cell development, Immunity, 37(5), 785-799 (2012).
(PubMed)

Harry Amri Moesa, Shunichi Wakabayashi, Kenta Nakai, and Ashwini Patil, Chemical composition is maintained in poorly conserved intrinsically disordered regions and suggests a means for their classification. Mol. Biosystems, 8(12), 3262-3273 (2012); published online on 18 Oct 2012
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Sumiyo Morita, Ryou-u Takahashi, Riu Yamashita, Atsushi Toyoda, Takuro Horii, Mika Kimura, Asao Fujiyama, Kenta Nakai, Shoji Tajima, Ryo Matoba, Takahiro Ochiya and Izuho Hatada, Genome-wide analysis of DNA methylation and expression of microRNAs in breast cancer cells, Int. J. Mol. Sci., 13(7), 8259-8272 (2012).
(abstract)

Daniel Kraut, Eitan Israeli, Erin Schrade, Ashwini Patil, Kenta Nakai, Dhaval Nanavati, Tomonao Inobe, and Andreas Matouschek, Sequence- and species-dependence of proteasomal processivity, ACS Chemical Biology,7(8), 1444-1453 (2012); epub 2012 Jun. 22.
(abstract)

Kouichi Kimura, Asako Koike, and Kenta Nakai, A Bit-parallel dynamic programming algorithm suitable for DNA sequence alignment, J. Bioinformatics and Computational Biology, 10(4), 1250002 (2012); published online on Feb. 2, 2012.
(abstract)

Riu Yamashita, Sumio Sugano, Yutaka Suzuki, and Kenta Nakai, DBTSS: database of transcriptional start sites progress report in 2012, Nucl. Acids Res., 40(Database Issue), D150-154 (2012); published online on Nov. 15, 2011.
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